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CLEC4F Gene

protein-coding   GIFtS: 45
GCID: GC02M071035

C-Type Lectin Domain Family 4, Member F

(Previous names: C-type (calcium dependent, carbohydrate-recognition domain)...)
(Previous symbol: CLECSF13)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
C-Type Lectin Domain Family 4, Member F1 2     C-Type Lectin Superfamily Member 132 3
CLECSF131 2 3     KCLR2
C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin,
Superfamily Member 131 2
     C-Type Lectin Domain Family 4 Member F2
C-Type Lectin 132 3     

External Ids:    HGNC: 253571   Entrez Gene: 1655302   Ensembl: ENSG000001526727   UniProtKB: Q8N1N03   

Export aliases for CLEC4F gene to outside databases

Previous GC identifers: GC02M070948 GC02M070889 GC02M070772


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CLEC4F Gene:
CLEC4F (C-type lectin domain family 4, member F) is a protein-coding gene. Diseases associated with CLEC4F include ataxia, and hepatitis. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is CD207.

UniProtKB/Swiss-Prot: CLC4F_HUMAN, Q8N1N0
Function: Receptor with an affinity for galactose and fucose. Could be involved in endocytosis (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the CLEC4F gene promoter:
         HNF-4alpha2   Tal-1beta   E4BP4   E47   HNF-4alpha1   SRY   POU2F1   POU2F1a   ZID   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC4F promoter sequence
   Search Chromatin IP Primers for CLEC4F

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC4F


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p13.3   Ensembl cytogenetic band:  2p13.3   HGNC cytogenetic band: 2p13.3

CLEC4F Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC4F gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M071035:  view genomic region     (about GC identifiers)

Start:
71,035,775 bp from pter      End:
71,047,732 bp from pter
Size:
11,958 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CLC4F_HUMAN, Q8N1N0 (See protein sequence)
Recommended Name: C-type lectin domain family 4 member F  
Size: 589 amino acids; 65519 Da
Sequence caution: Sequence=BAC04786.1; Type=Erroneous termination; Positions=540; Note=Translated as Trp;

Explore the universe of human proteins at neXtProt for CLEC4F: NX_Q8N1N0

Explore proteomics data for CLEC4F at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn79, Asn113, Asn207, Asn230, Asn244, Asn312, Asn385, Asn399
  • Modification sites at PhosphoSitePlus

  • See CLEC4F Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001244956.1  NP_775806.2  

    ENSEMBL proteins: 
     ENSP00000272367   ENSP00000390581  

    CLEC4F Human Recombinant Protein Products:

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    CLEC4F Assay Products:

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    Cloud-Clone Corp. CLIAs for CLEC4F


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CLEC: C-type lectin domain containing

    3 InterPro protein domains:
     IPR016187 C-type_lectin_fold
     IPR016186 C-type_lectin-like
     IPR001304 C-type_lectin

    Graphical View of Domain Structure for InterPro Entry Q8N1N0

    ProtoNet protein and cluster: Q8N1N0

    UniProtKB/Swiss-Prot: CLC4F_HUMAN, Q8N1N0
    Similarity: Contains 1 C-type lectin domain


    CLEC4F for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLC4F_HUMAN, Q8N1N0
    Function: Receptor with an affinity for galactose and fucose. Could be involved in endocytosis (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030246carbohydrate binding IEA--
         
    CLEC4F for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Clec4f):
     hematopoietic system  immune system 

    CLEC4F for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLEC4F
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLEC4F
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    hsa-miR-186* hsa-miR-3176 hsa-miR-1224-5p hsa-miR-103a-2* hsa-miR-3922-3p
    SwitchGear 3'UTR luciferase reporter plasmidCLEC4F 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CLEC4F

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    Clone
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    Sino Biological Human cDNA Clone for CLEC4F
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC4F

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC4F


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLC4F_HUMAN, Q8N1N0: Membrane; Single-pass type II membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1
    extracellular1
    mitochondrion1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    CLEC4F for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CLEC4F
    Interactions:

        Search GeneGlobe Interaction Network for CLEC4F

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for CLEC4F (Q8N1N02, 3 ENSP000002723674) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATXN1P542532, 3, ENSP000002447694MINT-2879054 MINT-2879073 I2D: score=3 STRING: ENSP00000244769
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006897endocytosis IEA--

    CLEC4F for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CLEC4F (CLC4F)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CLEC4F gene (2 alternative transcripts): 
    NM_001258027.1  NM_173535.2  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000272367(uc002shf.3 uc010yqv.1) ENST00000426626
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate CLEC4F:
    hsa-miR-186* hsa-miR-3176 hsa-miR-1224-5p hsa-miR-103a-2* hsa-miR-3922-3p
    SwitchGear 3'UTR luciferase reporter plasmidCLEC4F 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for CLEC4F
    Predesigned siRNA for gene silencing in human, mouse, rat CLEC4F
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    GenScript: all cDNA clones in your preferred vector: CLEC4F (NM_173535)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLEC4F
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC4F
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for CLEC4F
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLEC4F
      QuantiTect SYBR Green Assays in human, mouse, rat CLEC4F
      QuantiFast Probe-based Assays in human, mouse, rat CLEC4F

    8 AceView cDNA sequences:

    BM720443 NM_173535 BU740367 AK096429 CK003546 BU739898 BM725640 CD701685 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLEC4F expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCCAGGGTG
    CLEC4F Expression
    About this image


    CLEC4F expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Liver (Hepatobiliary System)    fully expand to see all 2 entries
             Mature Mesothelial Cells Hepatic Mesenchyme
             Liver Lobule
    CLEC4F Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLEC4F Protein Expression
        Custom PCR Arrays for CLEC4F
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC4F

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CLEC4F gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clec4f1 , 5 C-type lectin domain family 4, member f1, 5 69.33(n)1
    55.21(a)1
      6 (35.94 cM)5
    518111  NM_016751.31  NP_058031.21 
     836445425 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 4)
    Uncharacterized protein
    (see all 4)
    30(a)
    29(a)
    (see all 4)
    many ↔ many
    many ↔ many
    (see all 4)
    GL343830.1(152731-155973)
    GL343540.1(119051-134906)
    zebrafish
    (Danio rerio)
    Actinopterygii CD2076
    CD207 molecule, langerin
    17(a)
    1 → many
    8(41685924-41692286) ENSDARG00000046142


    ENSEMBL Gene Tree for CLEC4F (if available)
    TreeFam Gene Tree for CLEC4F (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLEC4F gene
    CD2072  CLEC17A2  CLEC4E2  ASGR22  CLEC4M2  CD2092  CLEC4A2  FCER22  
    CLEC10A2  CLEC6A2  ASGR12  CLEC4C2  CLEC4D2  CLEC4G2  
    1 SIMAP similar gene for CLEC4F using alignment to 3 protein entries:     CLC4F_HUMAN (see all proteins):
    CD207

    CLEC4F for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CLEC4F
    PGOHUM00000250430


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CLEC4F (see all 479)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3704186001,2
    C--70777090(+) TCTTT-/TTCTTTC 2 -- int10--------
    rs599237901,2
    C--71035335(+) CACTTC/TGGCAG 2 -- int1 ds50011Minor allele frequency- T:0.50WA 2
    rs1931917661,2
    --71035384(+) AACAGA/CCTGGC 2 -- int1 ds50010--------
    rs788699991,2
    C--71035392(+) GGCCAG/ACATGG 2 -- int1 ds50011Minor allele frequency- A:0.50CSA 2
    rs1112430481,2
    F--71035600(+) AGTCCC/TTGTAG 2 -- int1 ds50011Minor allele frequency- T:0.50CSA 2
    rs1447281741,2
    --71035617(+) TTCAAC/TCTCTG 2 -- int1 ds50010--------
    rs1872248871,2
    --71035709(+) TGAGGA/GAAGGA 2 -- int1 ds50010--------
    rs1912525161,2
    --71035776(+) AAGCTG/TTTGTT 2 -- ut310--------
    rs1837797921,2
    C--71035928(+) GAATCA/GAAGAA 2 -- ut310--------
    rs1477926631,2
    C--71035951(+) TCCAC-/AAGGCC 2 -- ut310--------

    HapMap Linkage Disequilibrium report for CLEC4F (71035775 - 71047732 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CLEC4F:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv458130CNV Loss19166990

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLEC4F
    DNA2.0 Custom Variant and Variant Library Synthesis for CLEC4F

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases for CLEC4F:    
    About MalaCards
    ataxia    hepatitis


    CLEC4F for disorders           About GeneDecksing


    Export disorders for CLEC4F gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CLEC4F gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CLEC4F)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1, 3 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
    3. Structure of the gene for a carbohydrate-binding receptor unique to rat kupffer cells. (PubMed id 1846367)1, 3 Hoyle G.W. and Hill R.L. (J. Biol. Chem. 1991)
    4. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (Cell 2006)
    5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 165530 HGNC: 25357 AceView: CLECSF13 Ensembl:ENSG00000152672 euGenes: HUgn165530
    ECgene: CLEC4F H-InvDB: CLEC4F

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CLEC4F Pharmacogenomics, SNPs, Pathways
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_00114

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLEC4F gene:
    Search GeneIP for patents involving CLEC4F

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     EMD Millipore genomic analysis products

      
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